Silver nanoparticles (AgNPs) with different sizes have been extensively adopted in various commercial products, causing ecological concerns because of the inevitable release of AgNPs into the environment. Hence, understanding the interaction of different-sized AgNPs with environmental substances is important for assessing the environmental risk and fate of AgNPs. In this work, we investigated the impact of anions (NO3−, SO42−, HCO3−/CO32−, Cl−) in aquatic environments on the physicochemical properties and antibacterial activity of different-sized AgNPs (20, 40 and 57 nm). The results showed that the anions whose corresponding silver-based products had lower solubility were more likely to decrease the zeta potential (more negative) of particles, inhibit the dissolution of AgNPs and reduce their antibacterial activity. This should be attributed to the easier generation of coating layers on the surface of AgNPs during the incubation process with such anions. Additionally, the generation of coating layers was also found to be particle-size dependent. The anions were more prone to adsorbing onto larger-sized AgNPs, promoting the formation of coating layers, subsequently resulting in more pronounced variations in the physicochemical properties and antibacterial activity of the larger-sized AgNPs. Therefore, larger-sized AgNPs were more prone to experiencing specific effects from the anions.